The major aim in our program is to relate structure and biological function of nucleic acids. The effects of chemically well defined modifications of the pyrimidine nucleotides are investigated under in vitro and in vivo conditions. Bacterial and mammalian systems are used. Major attention has been focused on the effects on nucleic acid structure and function of the saturation of the 5,6-double bond of the pyrimidine bases which leads to a decrease in their stacking and base pairing capabilities. Saturated pyrimidine nucleotides are found naturally in transfer RNA (5,6-dihydrouridine) and are formed in RNA and DNA following exposure to ultraviolet or ionizing radiation and certain mutagens (e.g., hydroxylamine). As part of this program we have studied (1) the chemistry and biological function of 5,6-dihydrouridine in transfer RNA, (2) the effects of the introduction of N4-acetyl-tetrahydrocytidine into polycytidylic acid on its conformation, (3) the effect of uridine- and cytidine photohydration (i.e., formation of 6-hydroxy-5,6-dihydrouridine and 6-hydroxy-5,6-dihydrocytidine) on the infectivity of coliphage R17 and the messenger activity of R17-RNA, (4) the chemistry of deoxycytidine photohydration in DNA, (5) the radiation chemical reactivity of thymine (i.e., the formation of products of the 6-(hydroxy or hydroperoxy)-5,6-dihydrothymine type) in HeLa chromatin and nucleoprotein preparations, and (6) the removal from the DNA of gamma-ray damaged thymine residues of the 6-(hydroxy- or hydroperoxy)-5,6-dihydrothymine type during postirradiation incubation of Chinese hamster ovary cells.